Package: methylInheritance 1.37.0

Astrid Deschênes

methylInheritance: Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect

Permutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed.

Authors:Astrid Deschênes [cre, aut], Pascal Belleau [aut], Arnaud Droit [aut]

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manual.pdf |manual.html✨
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methylInheritance/json (API)
NEWS

# Install 'methylInheritance' in R:
install.packages('methylInheritance', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/adeschen/methylinheritance/issues

Datasets:
  • demoForTransgenerationalAnalysis - The methylation information from samples over three generations. Information for each generation is stored in a 'methylRawList' format (for demo purpose).
  • methylInheritanceResults - All observed and permutation results formatted in a 'methylInheritanceResults' class (for demo purpose).
  • samplesForTransgenerationalAnalysis - All samples information, formated by 'methylKit', in a 'methylRawList' format (for demo purpose).

On BioConductor:methylInheritance-1.37.0(bioc 3.24)methylInheritance-1.36.0(bioc 3.23)

biologicalquestionepigeneticsdnamethylationdifferentialmethylationmethylseqsoftwareimmunooncologystatisticalmethodwholegenomesequencinganalysisbioconductorbioinformaticscpgdifferentially-methylated-elementsinheritancemonte-carlo-samplingpermutation

4.88 score 6 scripts 452 downloads 9 exports 97 dependencies

Last updated from:a2ea86b980. Checks:1 WARNING, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING214
linux-devel-x86_64OK527
source / vignettesOK308
linux-release-x86_64OK514
macos-release-arm64OK302
macos-oldrel-arm64OK302
windows-develOK465
windows-releaseOK474
windows-oldrelOK470
wasm-releaseOK144

Exports:calculateSignificantLevelextractInfoloadAllRDSResultsloadConvergenceDatamergePermutationAndObservationplotConvergenceGraphplotGraphrunObservationrunPermutation

Dependencies:abindaskpassbbmlebdsmatrixBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopscigarilloclicodacodetoolscpp11crayoncurldata.tableDelayedArrayemdbookfarverfastsegformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegridExtragtablegtoolshttrIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmethylKitmgcvmimemvtnormnlmenumDerivopensslplyrqvalueR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlrebusrebus.baserebus.datetimesrebus.numbersrebus.unicodereshape2restfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystatmodstringistringrSummarizedExperimentsysvctrsviridisLitewithrXMLXVectoryaml

Inferring inheritance of differentially methylated changes across multiple generations

Astrid Deschênes, Pascal Belleau and Arnaud Droit

Rendered frommethylInheritance.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2018-11-30
Started: 2017-04-07